Variant report

Variant	rs4474240
Chromosome Location	chr1:154457855-154457856
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:154457376..154460470-chr1:154460552..154464074,3	K562	blood:
2	chr1:154456314..154458192-chr1:154933230..154935390,2	K562	blood:
3	chr1:154457376..154460470-chr1:154460552..154464074,4	K562	blood:
4	chr1:154456666..154458398-chr1:154524462..154526767,2	K562	blood:

Variant related genes	Relation type
ENSG00000169291	Chromatin interaction
ENSG00000163348	Chromatin interaction
ENSG00000229780	Chromatin interaction
ENSG00000160714	Chromatin interaction
ENSG00000271380	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10159236	1.00[CEU][hapmap];0.81[GIH][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes]
rs10752642	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10752643	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10908844	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10908846	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11265618	1.00[CEU][hapmap];0.83[MEX][hapmap]
rs11265627	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11265629	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11265634	0.91[EUR][1000 genomes]
rs11804305	0.85[EUR][1000 genomes]
rs12118074	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12124333	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12129484	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs14021	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16836054	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4074436	0.96[GIH][hapmap]
rs41302545	0.95[EUR][1000 genomes]
rs4131514	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4240873	0.83[YRI][hapmap]
rs4269769	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4288587	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4307559	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4307560	0.83[AFR][1000 genomes]
rs4308966	0.87[EUR][1000 genomes]
rs4329505	1.00[CEU][hapmap];0.81[GIH][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes]
rs4345796	0.86[EUR][1000 genomes]
rs4393148	0.89[ASW][hapmap];0.83[LWK][hapmap];0.94[MKK][hapmap];0.85[YRI][hapmap]
rs4518898	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4575077	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4585969	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845374	1.00[CEU][hapmap]
rs4845626	1.00[CEU][hapmap];0.83[MEX][hapmap]
rs4845632	0.83[ASW][hapmap];0.83[LWK][hapmap];0.94[MKK][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes]
rs4845634	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845635	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845636	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845640	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4845641	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845643	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4845644	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845646	0.83[ASW][hapmap];0.80[LWK][hapmap];0.94[MKK][hapmap];0.81[YRI][hapmap]
rs4845648	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56047170	0.89[EUR][1000 genomes]
rs56233546	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61811362	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61812599	0.84[EUR][1000 genomes]
rs61812626	0.86[EUR][1000 genomes]
rs61812631	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61812654	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427694	0.83[ASW][hapmap]
rs6427716	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427720	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6427721	0.85[AFR][1000 genomes]
rs6427722	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427724	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6656395	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6662503	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6670375	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6678164	0.80[LWK][hapmap];0.90[MKK][hapmap];0.81[YRI][hapmap]
rs6683078	0.83[ASW][hapmap];0.83[LWK][hapmap];0.90[MKK][hapmap];0.85[YRI][hapmap]
rs6684225	0.90[MKK][hapmap];0.81[YRI][hapmap]
rs6687112	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6689710	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6691727	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696177	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6697103	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6697115	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6701586	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6703672	0.91[EUR][1000 genomes]
rs72698167	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7513603	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7526247	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7539745	1.00[CEU][hapmap];0.84[YRI][hapmap];0.96[EUR][1000 genomes]
rs7543174	0.94[CEU][hapmap];0.96[GIH][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs7550664	0.94[EUR][1000 genomes]
rs7553602	1.00[CEU][hapmap];0.81[GIH][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes]
rs9427076	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9427082	0.95[EUR][1000 genomes]
rs9427415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9728545	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
2	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
3	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4474240	RPTN	cis	cerebellum	SCAN
rs4474240	DPM3	cis	cerebellum	SCAN
rs4474240	SNX27	cis	parietal	SCAN
rs4474240	CDC42SE1	cis	cerebellum	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154427800-154464800	Weak transcription	Ovary	ovary
2	chr1:154438400-154458400	Weak transcription	Gastric	stomach
3	chr1:154438400-154463400	Weak transcription	Esophagus	oesophagus
4	chr1:154440000-154458200	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr1:154441600-154465200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr1:154443000-154464400	Weak transcription	Colon Smooth Muscle	Colon
7	chr1:154447800-154458400	Weak transcription	Brain Angular Gyrus	brain
8	chr1:154448600-154458200	Weak transcription	Brain Substantia Nigra	brain
9	chr1:154450000-154462400	Weak transcription	Colonic Mucosa	Colon
10	chr1:154451600-154465600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr1:154452400-154458200	Weak transcription	Fetal Intestine Small	intestine
12	chr1:154452600-154458200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr1:154452800-154458000	Weak transcription	Brain Cingulate Gyrus	brain
14	chr1:154452800-154458200	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr1:154452800-154458400	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr1:154452800-154458400	Weak transcription	Duodenum Mucosa	Duodenum
17	chr1:154452800-154458400	Weak transcription	Fetal Stomach	stomach
18	chr1:154452800-154458400	Weak transcription	Stomach Smooth Muscle	stomach
19	chr1:154453000-154458200	Weak transcription	Liver	Liver
20	chr1:154453000-154458200	Weak transcription	Brain Anterior Caudate	brain
21	chr1:154453000-154458200	Weak transcription	Brain Hippocampus Middle	brain
22	chr1:154454000-154461800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr1:154454800-154458000	Weak transcription	Brain Germinal Matrix	brain
24	chr1:154455200-154461600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr1:154455600-154460200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr1:154456400-154458400	Enhancers	Hela-S3	cervix
27	chr1:154456400-154460200	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr1:154456600-154458200	Weak transcription	Psoas Muscle	Psoas
29	chr1:154456600-154458400	Weak transcription	Lung	lung
30	chr1:154456600-154458400	Weak transcription	Right Atrium	heart
31	chr1:154456600-154460200	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr1:154456800-154458200	Weak transcription	Right Ventricle	heart
33	chr1:154456800-154458400	Weak transcription	Left Ventricle	heart
34	chr1:154457000-154458200	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr1:154457000-154458200	Weak transcription	Spleen	Spleen
36	chr1:154457000-154459600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr1:154457000-154460000	Enhancers	Primary neutrophils fromperipheralblood	blood
38	chr1:154457200-154458400	Weak transcription	Fetal Muscle Trunk	muscle
39	chr1:154457200-154458600	Weak transcription	K562	blood
40	chr1:154457200-154459400	Enhancers	Primary hematopoietic stem cells	blood
41	chr1:154457600-154458000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr1:154457600-154458000	Bivalent Enhancer	NHEK	skin
43	chr1:154457600-154458600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr1:154457600-154459000	Enhancers	Placenta	Placenta
45	chr1:154457600-154459200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:154457600-154459200	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr1:154457600-154459200	Enhancers	Fetal Lung	lung
48	chr1:154457800-154458000	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr1:154457800-154458000	Enhancers	Monocytes-CD14+_RO01746	blood
50	chr1:154457800-154458200	Enhancers	HUVEC	blood vessel

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